Lucario is not a Mewtwo clone, that is plain as day, we also know that Lucario was also not meant to replace Mewtwo (at least by the end of development) through datamines - but I also think it's not that unreasonable to believe Lucario was meant to some kind of 'successor' to Mewtwo in aesthetic/diegetic role at least, or wasn't built off of either experience or data relating to Mewtwo in Melee. I'd say those two characters have a connection, but it's not the strongest. The same one as Mii Swordfighter and Hero, Mario and Ness, or ZSS and Bayonetta functionally; and all the non-trainer starters diegetically. Less "out with the old, in with the new" and more "that (in this case, a mysterious cool bipedal special-Pokemon) was recieved well, let's make lightning strike twice"
Also MechaMew2 - putting aside the obscurity of the character and lost nature of the source material - would not be able to work as a clone because of the catterpillar treads. They should put MechaMew2 in Smash though, hell yeah. Unless you're talking about Mewtwo's armour, which isn't really a seperate character, but... that'd be kinda neat. I know a lot of people want Mewtwo to be heavier and an armoured echo would be a good way to get that. I do wonder if Mewtwo's tail-to-hand move ratio is lopsided enough to where Mew's stubby arms wouldn't be a problem, at least not any more than Pichu's stubbier limbs and neck are for them.